Miss me?
by MusicalBlueFlame
Summary: How did that criminal survive the gun? This must be one of Sherlock's toughest cases. Multiple chapters.
1. How did he do it?

This is technically set after the reichenbach fall episode but we've had three episodes since then, this little story can slot in anywhere really, it won't be matching up to any of the series three stories. It's supposedly meant to be after the episode with Charles Agustus Magnussen but obviously there has to be something to do with why Sherlock was being arrested and everything and to be honest, I have no idea what happened there, Mary may come in somewhere as we go along but her story is now really complicated too, who is she really? Anyway, hope you enjoy it readers.

_"You can go, save your friends as while I'm alive they can still be saved, so sorry" Moriarty placed the gun in his mouth and shot, Sherlock leapt back stunned and frightened, he stepped off the edge._

Sherlock opened his eyes and looked up at the celling, snapping himself out of the flashback.  
>"John? How do you think he did it?"<br>"No Sherlock, don't bring this up again, you're the one who was on the roof, I was on the ground watching, I didn't even know Moriarty was up there with you until you told me what had happened."  
>"So you have no suggestions what so ever?"<br>"You're the detective" John shrugged and turned back to his book.  
>Sherlock drummed his fingers on his knee then gasped "I wasn't the only one thinking how I could fake my death, I can think of three ways he may have done it!"<br>John put down the book and looked patiently at his friend who was perched on his chair "well?"  
>"Remember those targets he was using to get to me, the people who were strapped to the bombs? There is a possibility that he used one of those with his identity, voice, personality, everything to make me believe I was talking to him."<br>"That's impossible Sherlock, the police found his body and identified him as Moriarty" John sighed.  
>"Nothing is impossible John, I survived."<br>"That's not the point Sherlock, you saw him shoot himself, it must've been an illusion."  
>"Brilliant John! That was my next conclusion, I thought about a blood capsule under the roof of the mouth where he shot but the blood came under the back of his head, unless..."Sherlock leapt up and made his way over to his board of solutions on the wall "what if he shot himself somewhere else on his body as a way of making me believe he shot himself when actually the bullet went nowhere near his head?"<br>"That's mad Sherlock, he would have had so much planning behind it, what if you had got in the way or something? All we know is that he's free again and he'll be coming after you, if he knows you're still alive, I dread to think" John shook his head and Sherlock frowned.  
>"What's wrong John?"<br>"I couldn't live through you leaving again Sherlock, you're my best friend" John didn't look up.  
>"I'm not letting Moriarty take me anywhere this time, if he wants to make a fight, he can have it, we'll be ready for him this time round" Sherlock made for the door flinging his coat on as he did.<p>

"Where are you going?"

"I need to talk to Molly, are you coming?"

"Well, if you need me to come along?"

"I prefer company."

"And someone to actually talk too other than yourself" John laughed to himself ignoring Sherlock's small pout.

As St Bart's came into sight John noticed Sherlock wince slightly as they drove past the front of the building, as the cab came to a halt Sherlock leapt out leaving John to pay, much to his annoyance. John found Sherlock in the morgue talking to Molly who was trying to sign papers.

"Please Molly, please remember every detail of Moriarty after the shooting" Sherlock persisted.

"It was hard Sherlock, all I can remember was that he had a hole through his head, he died as soon as that bullet went through."

"Impossible, he's still alive. You saw the message he left on every screen in London."

Molly sighed and put down her papers "you survived and that's all that matters, no, I don't mean it like that, it's just. I had a feeling you were going to survive even if you hadn't come to me with your plan, Moriarty is different, he died there, he just can't be alive."

"I can't figure it out, you saw him die Sherlock" John spoke up.

"Precisely, he shook my hand and shot himself before I could say anything, it's baffling" Sherlock sat down and ran his hands through his hair, Molly shared a worried look with John and went over.

"Sherlock, what's wrong?"

"Nothing is wrong, I'm fine, I hate not knowing."

Molly hesitantly rested her hand on Sherlock's shoulder, she relaxed a little when he un-tensed his shoulders "it's not a crime not to know, John and I don't care, we're just as puzzled as you."

"It's my job not to be 'puzzled'" Sherlock snapped.

Molly bit her lip "I…"

"I'm sorry Molly, it's not your fault."

"It's ok" Molly shrugged.

John cleared his throat "so what are we going to do about Moriarty?"

"We need to find him, I still have that number he gave me, though he may have changed it since our second meeting" Sherlock reached into his pocket and took out his phone.

"I don't think it's safe for you to stay at Baker Street for the moment, that's the first place he'll go looking for you" John said worriedly.

"You're right John, although I don't think staying in one of my hideouts would work this time, he'd seek me out."

"You're always free to stay at my place, Moriarty or Jim as I called him then, never found out where I staying, I've moved since anyway. Tom has gone as you already know."

"I didn't mean to bring up the breakup Molly, thank you for the offer, I will consider it" Sherlock smiled at her then indicated to John that they needed to go.

"I'm guessing you need a word with Lestrade?" John asked.

"You're getting better John" Sherlock grinned slightly and left the room leaving Molly feeling rather flushed with happiness.

"You can't be serious Sherlock" Lestrade sat frowning at the detective "Moriarty is dead, filed, and buried."

"So was I if you remember."

"That's not the point Sherlock you were technically never dead. You told me exactly what happened on that rooftop, don't now tell me that it was an illusion."

"Inspector, I am, for the first time, clueless to how he is still alive, that's why I have come to you for suggestions, John's suggestions weren't helpful."

"They were yours" John looked up raising his eyebrows.

"Shh. Well, Lestrade, let's hear them?" Sherlock sat down and cupped his hands under his chin.

"Well, you say he shot himself through the head, there could've been a spot that he hit which caused him to die momentarily" Greg paused watching Sherlock narrow his eyes "or a mirage, but I can't see a way he could have pulled that off."

"Sherlock, did he seem to have a plan?" John asked breaking the silence in the office.

Sherlock looked away from Lestrade very quickly and almost grinned "John, that is a fantastic question."

"I'm sorry, a minute ago you were ruling out any possibility of him being alive or dead for that matter, and now…"

"Don't you see, I should have thought of this straight away! That day, it was I who was the scared one on the roof, he was too calm, too calm for someone about to take their own life."

"Where is this going Sherlock?" Lestrade asked impatiently leaning back in his chair.

"He had a plan all along, I can read ordinary people like a book, but Moriarty, he was different."

"An actor" John gasped.

"Exactly John" Sherlock smiled.

"So you're telling me that the whole shooting in the head was an act, like a scene from a play?"

"Precisely, all we need now is proof, come on John, we need to track down a Mr Moriarty" without a word of goodbye, Sherlock was out of the door, John nodded at Lestrade and followed quietly after.

Later that afternoon Sherlock awoke from his daydream and called out to John who, still out buying groceries, didn't answer. Instead Mrs Hudson walked in.

"Is something wrong dear?"

"Where's John?"

"He's gone out, actually he's been gone for the last hour, where do you go which stops you concentrating on life?"

Sherlock shrugged "it keeps me occupied?" He got up quickly and grabbed John's laptop off the table.

"Something is bothering you" Mrs Hudson frowned.

"Moriarty, he's already trying to get my attention" Sherlock muttered ignoring Mrs Hudson's tremor at Moriarty's name.

"Promise me Sherlock, you won't go after him?"

"I've stopped him once, I can stop him again."

"I don't want you to stop him the way you did before. What it did to me, and John. Your only best friend."

Sherlock pretended to ignore her and continued to focus on the top crimes of Moriarty over the last couple of days.

"I got the groceries you needed Mrs Hudson. Are you alright here?" John asked suddenly noticing the stillness in the room as he entered.

"Ah John, I didn't notice you had gone out."

"You never do."

"Whatever, I need your help over Moriarty, you have to help me think of a way I can become bait for him" Sherlock looked away from the screen and to his wall of 'rats'. Mrs Hudson sighed and left the room in disgust.

"No, no bait. God sake Sherlock, I've…we've just got you back, don't give yourself up already!"

"I need to know John, doesn't it not bother you that he is still alive?"

"No, it bothers me that you're so obsessed over this, it's not like it's a case or anything, this is a sick hobby which will get you killed again" John shook his head and turned away to put the groceries on the table.

"If you won't help me, I'll ask M.."

"I've already discussed it with her and she's not helping you to kill yourself again or anything which will get her tied up in Moriarty's plans, whatever they are."

"When did she say this?"

"While you were playing in your mind palace, I contacted her. Do you not care about her feelings, affections?"

"Affections?" Sherlock frowned.

"Yes affections, she cares about you and sharing your death plan with her, upset her."

"But she helped me."

"It doesn't mean she enjoyed watching you fall to your imaginary death. That's all. She won't be helping this time round, even if you ask her personally. I'm taking a shower, just think about what I've said."


	2. Apologies

Sherlock sat speechless in his chair and tried to think back to his fall and what he had told Molly.

_"Molly, I think I'm going to die."_

_"What do you need?"_

_"You."_

_"What do you need me to do Sherlock?"_

_"I need someone to help me pull off something ridiculously drastic, to fake my own death, somehow…"_

Sherlock remembered watching Molly's eyes widen in horror.

_"Fake your death, what do you mean?"_

_"I believe Moriarty is going to try and kill me up on the roof of this hospital, this is where everyone gets involved, including you."_

_"I don't understand, who's everyone?"_

_"My brother, some of my homeless network,"_

_"Does John know about this?"_

_"No. Molly, please promise you won't say a word to him about this."_

_"This doesn't feel right Sherlock."_

_"Molly, you're the key to this whole operation and one of the only people I know I can really trust…"_

Sherlock opened his eyes and a tear fell down his cheek, he shook his head trying to erase the flashback, had he really not noticed the pain he had just caused Molly to feel? Without a word or goodbye to John, he left the house, John returned moments later to the lounge and called out to Sherlock, there was no answer, then he noticed a sheet of paper on the desk, he went over and read it to himself.

_'John,_

_I have a lot of apologising to do, I will be back either late or early tomorrow morning._

_I'm sorry for the hurt I have caused you in the past._

_Sherlock.'_

After a short ride Sherlock arrived at his destination, he paid the driver and got out of the cab. He looked up at the house he was now outside, there appeared to be no-one in but through a small crack in the curtains of the front room a small stream of light was peeking out, he made his way to the door and rang the bell once half wanting the owner not to be in, then the door opened.

"Sherlock?!" Molly exclaimed softly.

"Molly, this probably isn't the best time, but I've come to…"

"Is someone after you?"

"No, don't worry, I just want to apologise for the way I've treated you these last two years."

Molly smiled "come in Sherlock, please."

Molly led him into the lounge and offered him tea which he politely refused.

"You don't need to keep apologising Sherlock, I forgive you, really I do."

"I was thinking about what I asked you that day, it wasn't fair, I shouldn't have put you in that position, I forced John to leave but not you, I made you watch" Sherlock looked away from Molly's eyes.

"Sherlock, I'm glad I helped you, as soon as I knew you were going to make it and survive, I stopped worrying, yes it was terrible watching you fall past the window but everything below was in place, nothing to worry about."

"Molly" Sherlock started but Molly cut him off.

"Stop, you've got other matters to deal with, Moriarty being alive is one of them, make him your top priority, not me" Molly smiled.

"You're always my top priority" Sherlock said quietly rubbing his hands together nervously, he felt Molly's fingers on his hands and he turned to face her.

"You are a very complicated man Sherlock, and since the first time I started working with you, I have, always admired you."

Sherlock took her chin in his hand and gently kissed her, Molly closed her eyes and laid her hand on the back of his neck lovingly.

"Are you going back to Baker Street tonight?" Molly asked between kisses.

"No, I'll take the spare bedroom if that's alright?" Sherlock smiled.

"No need."

Back at Baker Street Mrs Hudson and John were talking.

"Where do you think he's gone?"

"You know Sherlock, never leaves a location with his disappearances."

"Maybe I was a little too harsh on him about Molly and the fall."

"Don't blame yourself John, he needs to be told sometimes, anyway it's better if he hears it from friends."

John sighed "I hope he returns in the morning, I'm off to bed. Goodnight Mrs Hudson."

"Goodnight John, don't worry about Sherlock, he'll come back."

"He always does."

_Author's note: this one is a little shorter but at least there's some mystery, will Sherlock go back to Baker Street in the morning or will something change his mind? Poor John, thinking it's his fault, it isn't John don't worry :) Thanks for following this story so far fanfic lovers x_


	3. An unexpected visitor

The next morning Sherlock awoke with Molly snuggled up against his arm, she opened her eyes slowly as she felt Sherlock get up.

"Do you have to go back to Baker Street?"

"Afraid so Molly, I can't leave John for too long" Sherlock grinned.

"Alright, will you be visiting me at Bart's today?" Molly asked blinking as the sun came through the window.

"Maybe. So, I will see you, later" Sherlock kissed her lightly then picked up his stuff to leave. Molly smiled then started to get ready for work.

Back at Baker Street John was standing by the window awaiting Sherlock's return, he had texted him countless times but there had been no reply all night, then a cab pulled up outside and Sherlock got out, up at the window John breathed a sigh of relief.

Sherlock came in and immediately apologised, much to John's surprise, then moved to his chair.

"Where were you Sherlock?"

"Around town, then I went to one of my hide outs to sleep. I knew you couldn't spend the night without worrying about me though, so I came back."

"You were at Molly's you mean?" John said in amusement.

"What do you mean?" Sherlock frowned.

"Her house is one of your hideouts, pretty obvious since the other hideouts are nowhere near here. Look Sherlock if I upset you, I'm sorry" John smiled as Sherlock rolled his eyes.

"I don't get upset John, you know too well I never let my emotions get the better of me."

"We both know that's not true" John chuckled lightly.

For a moment the pair sat in silence then the door bell rang causing them to jump.

"Once."

"Confident."

"Client?" John asked turning towards the door.

"No, this is someone with information" Sherlock smiled then returned to staring into space, when the door opened and the visitor came in, John stood up in haste.

"Good to see you again Sherlock."

Sherlock's eyes widened in horror as he turned to 'welcome,' the guest "Moriarty."

"So, you're alive too I see, must say I am a little disappointed, no matter, my men can fix that. Still with this lunatic I see John?" Moriarty sneered.

"What are you doing here? How can you be here?" John hissed.

"Oh, just paying dear Sherlock a visit, heard you've been a very busy bee. Terrorism, a wedding… The fun never seems to end."

"And what are you planning to do with me this time?" Sherlock asked raising his eyebrows slightly "kill me again?"

"That would be foolish seeing as that I've killed you once already and 'you only live twice Mr Holmes" Moriarty laughed stressing John more "no, this time I am going to completely destroy you, no getting people involved."

"Sherlock and I will stop you again Moriarty."

"Awwh John, if I remember correctly, you weren't even trusted with your friend's decision last time, how you think you'll be able to prevent the next is beyond me."

"You haven't even told us how you did it!"

"Mr Watson, I do believe Sherlock here still hasn't told you how he really did it, has he?"

John turned silent and glanced at Sherlock who suddenly looked very guilty.

"If he won't tell, I won't" Moriarty continued stretching out on the sofa "I have my own personal networker to tell me everything, have you, Sherlock?"

"Why would I need one when I have a dozen?"

"That's not true, I wouldn't call a bunch of homeless teens and adults a network, just beggars for news."

"And who is this networker?" John asked.

"Why would I tell you John Watson? I wouldn't want to give you a head start. Although, I'll give you a clue, she's a keeper" Moriarty winked and got up "I'll be around you two, I look forward to our next meeting" and with that he left closing the door behind him.

John sighed angrily "he sets my teeth on edge, what does he mean destroy you? He did that two years ago."

"A woman."

"And why doesn't he want us to know how he survived, more to the point, how you did? Sherlock? Are you even listening to me?"

"That narrows it down to four; Irene, Janine, Mrs Brooks and Mary" Sherlock rested his chin on his hands.

"Do not bring my wife into this Sherlock, don't make our relationship anymore unstable than it already has been since you returned."

"Sorry?"

"For God's sake! Mary is not working for Moriarty. I know that."

"We can't rule out the possibilities John, she's up against others don't worry" Sherlock shook his hand in missing out John's disagreement and carried on thinking to himself.


	4. The final problem

"Why do you think Mary is involved?" John remained persistent.

"She got involved with Magnussen, and she has an unknown past."

"So?"

"So, part of that past could be Moriarty."

"Oh for god's sake, she's finished with the undercover work."

"Has she told you why she shot me?"

"No."

Sherlock sat back and smiled to himself pissing John off more "would you like me to tell you?"

"I'm done, I can't sit here listening to this crap, Mary is not part of this and never has been."

Meanwhile across London, Mary was somewhat occupied with another.

"So, what am I to do with this plan?"

"I want you to destroy him, with me. You've shot him once before without hesitation, you can do it again."

"He returned though."

"I know Mrs Watson, but this time he won't. It'll be the end for Sherlock Holmes."

"And what about my husband, he must've get harmed, it's not part of the deal?" Mary frowned.

"I can't guarantee he'll be unhurt."

"I want a promise."

"Alright, but if he sides with Sherlock, I'll have no choice, and neither will you. Understand?"

Mary sighed in defeat "you have my word."

"I look forward to our next meeting, now run along, I'm sure John is waiting for you my dear."

Mary stood up and left feeling uneasy, turning against her husband's best friend, as she got home she noticed the lights were on.

"John?" she called closing the door "you here?"

"Mary. Where have you been?"

"John, I thought you were with Sherlock tonight?"

"He's driving me up the wall, he's fixed on Moriarty, and this time he's not going to stop until he's gone for good."

Mary bit her lip subtly "really?"

"He also thinks you're involved, along with Irene, Janine and some woman we came across a few years ago."

"Me? That's ridiculous!" Mary laughed self-consciously.

"That's what I told him."

"And well?"

"He told me not to rule out the possibilities."

"Well, I can assure you, I'm not working with Moriarty, I've lied to you once, I won't do it again" Mary smiled feeling horrible inside.

"That makes me feel a lot better" John smiled then frowned as he felt phone buzz in his pocket.

"Sherlock?" Mary asked.

"Yeah, asking where I am."

"Don't tell him, it's none of his business at the moment."

"He'll find out sooner or later, he may as well know" John laughed replying to the text, no sooner did it send did he get another from Sherlock.

_'Do you want to talk?'_

"Sorry Mary, he wants to discuss tonight, go up to bed and I'll join you soon."

Mary sighed and left the room, John called Sherlock and closed the door.

"What do you want Sherlock?"

"I've narrowed the names down to two suspects. Mary and Kitty."

"I'm going to hang up Sherlock if you say Mary is part of this, she's just told me herself that she is not with Moriarty."

"Obviously she is, you never notice the smallest of details."

"Sherlock, shut up I swear to God."

"Come round tomorrow and I'll explain everything, bring Mary with you" Sherlock hung up leaving John fuming.

That night John couldn't sleep, Mary couldn't be working with Moriarty, she wouldn't betray him again, she just couldn't. Sherlock didn't know, why was he trying to mess with his feelings?

The next day John headed back to Baker Street with Mary who was not happy about going.

"John, what is this about?"

"I have no idea, Sherlock wants to talk to me and told me to bring you with me" John sighed and opened the door, in the lounge Sherlock was playing the violin behind him he heard John enter.

"Morning John, Mary."

"Sherlock what is this about?" Mary asked frustrated.

Sherlock put the violin down on the chair beside him "this case is driving me insane, I've already had a visit from Moriarty, and he told John and me that he had a companion to help him with his plans, a woman, I believe you are working with him."

"Ok, my past has been messed up but I am not working with that maniac."

Sherlock read her again, one word flashed up 'liar' "you're not telling me the truth Mrs Watson."

"Of course I am."

"I can read you like a book."

"Sherlock, can we not do this?"

"John, I'm afraid he wants too" Mary closed her eyes and drew out her tranquiliser gun, one shot for Sherlock and with a small sob, one for John. They lay motionless on the floor and Mary phoned Moriarty.

When the two eventually came around John found himself tied to a wooden post and his mouth covered, he looked over at Sherlock opposite who's hands were tied behind his back.

"Don't worry John, we'll get out of here."

John rolled his eyes and muttered to himself "yeah right."

"Well, I must say this is a surprise, looks like Christmas has come early, and you've brought John" Jim laughed stepping into the pool of light.

"Moriarty, why did you bring Mary into this?"

"Oh, she chose to help me, you see she joined me before any of us knew you were alive, so it's not her fault at all. I'm sure John would like a say in this" Moriarty walked over and removed the rope from John's mouth.

"How could you?" John spat.

"Who are you asking, your wife or me?"

"Both."

"John" Sherlock warned.

"Stay out of this Sherlock!"

"John, I'm sorry" Mary sobbed "I know I've lied once before but..."

"I don't want to hear it, Sherlock and I have put our lives on the line for you Mary, I married you for trust and love, then you shoot Sherlock because he wants to help you, now I see who I can really trust and who I'd rather leave."

Sherlock looked watching Moriarty's change of expression.

"And you also know when you've got it wrong" Moriarty pulled out his gun and fired.

Mary screamed and jumped in front of John, the bullet caught her and she fell to her knees in pain.

"Mary!" John yelled pulling at his bonds.

Moriarty loaded the gun again intending the next bullet for Sherlock "we had a deal Mrs Watson, remember?" suddenly he felt his throat seize, Sherlock was standing behind him, his hands tight around Moriarty's neck. The breath left Jim and he collapsed to the floor, Sherlock untied himself and checked Moriarty's pulse, there wasn't one.

"Sherlock, untie me quickly!" John cried as Mary grew weaker by the second Sherlock undid the rope and John ran forward to his wife "call an ambulance now. Do it!"

"John, we'll be arrested if we do that."

"Christ sake Sherlock, this is my wife we're talking about."

"He's right John. Leave me please, when I'm found they'll trace all my past, I don't want you getting in trouble like that."

"I won't leave you" John moaned holding her to his chest.

Sherlock sat down on the floor and cupped his chin in his hands "at least you're innocent on murder, you didn't shoot us."

Mary coughed a small laugh "no really. Leave me, get out of here, John please."

John looked into her eyes and read the whole truth "I'll never forget you, my wife."

"Follow me John, and once we've outside call Molly, she'll know what to do, wait, I'll call her."

John stood up heartbroken and angry kissing Mary before turning to run out with Sherlock.

"Sherlock?" Molly's voice came down the phone.

"Mary's been shot by Moriarty and I've murdered Moriarty, we need an ambulance but John and I don't want to be arrested.

"Leave it to me, get back to Bart's, I'll meet you there later today, I'll get Mary and Moriarty."

"Thank you."

"No problem" Molly kissed him down the phone then hung up "John, we need to get back to Bart's, Molly will meet us there later…John?"

John was leant by the wall covering his eyes, Sherlock walked over slowly until he awkwardly hugged his friend.

"She was everything to me Sherlock, she got me through your death, married, supported my job. And now I find out again that she was lying the entire time, just to get to you."

"I'm so sorry John, I'm sorry I got you both dragged into this."

"Why are you blaming yourself?"

Sherlock turned away for a second to wipe his own tears away "by keeping secrets away from you about her, why she was a target."

"I forgive you Sherlock."

"Really?" Sherlock said tearfully.

"Of course, it's myself I can't forgive. I got so angry with her for no reason when I should've loved her for who she was. C'mon, let's get going" John breathed in and started to walk towards the main road, Sherlock followed slowly behind.

Once they got to the hospital they headed straight to the morgue, shortly after arriving Molly came in signing off the papers for Jim and Mary.

"John, I'm afraid we couldn't save her, but she told me to tell you that she loved you so much and that you were the best thing to happen in her life" Molly sniffed and Sherlock wrapped his arms her earning a surprised look from John.

"Thanks Molly, I'll be out later."

"Sherlock you did it. Defeated Moriarty" Molly smiled stroking his cheek.

"Did I? Or did I just cause my best friend a pain he will never lose?" Sherlock sighed.

"He will forgive you, you haven't stopped his heart, and you're not life ruiner, I know that" Molly closed her eyes with a sigh, she felt Sherlock's lips on hers and kissed him back.

"At least Moriarty can never return" Sherlock smiled running his hand through her hair.

"He never will, not with you still around" Molly smiled leaning against her friend, colleague, love.


End file.
